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2019中国化学会第十五届全国计算（机）化学学术会议

作者： Pengfei Li Xiangyu Jia Fengjiao Liu Xiaoliang Pan Meiting Wang Wei Liu Yihan Shao 梅晔 State Key Laboratory of Precision Spectroscopy School of Physics and Electronic Science East China Normal University Department of Chemistry and Biochemistry University of Oklahoma 华东师范大学

free energy calculations at an ab initio QM/MM level are a daunting challenge, due that extensive phase space sampling is always indispensable before convergence can be reached and for most cases many intermediate states are required to make the conversion between two states smooth enough. Recently, we proposed a reference-potential method for the calculations of PMF at high QM/MM levels using phase space sampling under low level Hamiltonians followed by free energy corrections from the low level to the high level Hamiltonians. Most of the time, a mixed non-Boltzmann ensemble from enhanced sampling such as replica exchange and umbrella sampling is used. For these cases, the non-uniform weight for each sample from Multistate Bennett Acceptance Ratio analysis should be considered in the free energy correlation calculations using thermodynamic perturbation. The efficiency of this method has been demonstrated in the free energy profile calculations for several toy reactions and Diels-Alder reactions in condensed phase. In general, a two-order of magnitude enhancement in efficiency can be observed. This idea can also be applied to adaptive QM/MM calculations for chemical reactions with solvent molecules strongly involved.

关键词： free energy profile QM/MM Multistate Bennett Acceptance Ratio Thermodynamic Perturbation

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Mutants only Partially Represent Characteristics of Calcium-ReleaseActivated Calcium Channel Gating

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Chinese Journal of Chemical Physics 2021年第6期34卷 915-924,I0005页

作者： Jun Huo Ben-zhuo Lu Hao Dong Kuang Yaming Honors School Nanjing UniversityNanjing 210023China CEMS LSECNCMISAcademy of Mathematics and Systems ScienceChinese Academy of SciencesSchool of Mathematical SciencesUniversity of Chinese Academy of SciencesBeijing 100190China Institute for Brain Sciences Nanjing UniversityNanjing 210023China State Key Laboratory of Analytical Chemistry for Life Science Nanjing UniversityNanjing 210023China Engineering Research Center of Protein and Peptide Medicine of Ministry of Education Nanjing UniversityNanjing 210023China

Calcium-release-activated calcium(CARC)channels are one of the major pathways of calcium entry in non-excitable *** a decade or two of research,its regulatory mechanism is not yet thoroughly *** slow progress is due to the complexity of its pores(i.e.,Orai)on one hand and the difficulty in capturing its regulatory complex on the other *** a result,possible gating mechanisms have often been speculated by exploring the structure and properties of constitutive open ***,there is much debate about how they can truly reflect the gating of CRAC channels under physiological *** the present study,we combined molecular dynamics simulations with free energy calculations to study three dOrai mutants(G170P,H206A,and P288A),and further calculated their current-voltage *** show that these constructs adopt different approaches to maintain their conductive *** they have unique pore structures and distinctive rectification properties and ion selectivity for cations compared to wild-type *** conclude that although the mutants may partially capture the gating motion characteristics of wild-type pores,the information obtained from these mutants is likely not a true reflection of CRAC channel gating under physiological conditions.

关键词： Calcium-release-activated calcium channel Gating mechanism Molecular dynamics simulations Mutant free energy profile

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